.pepXML not found using PDnode (PD2.2)

[schoofe]

Many thanks to the Nesvizhskii lab for releasing these awesome tools!

I'd be very keen on running MSFragger through our PD2.2 server, and managed to get the nodes up and running. The only problem is when trying a search (using a .mzml input file converted from a Thermo .raw file), the processing workflow errors out as it cannot find the .pepxml file that should be located in the "temp" folder. The only files present in this folder at that point are "fragger.params", the actual FASTA file and the .pepindex for that FASTA file.

Any input as to what I can do to debug this issue would be really appreciated, many thanks.

PD2.2 running on Windows 7, 64bit

[huiyinc]

Hi~

Could you please check if you have JRE8 installed in your computer?! One simple solution to check it is to download our FragPipe (https://github.com/Nesvilab/FragPipe) and run it for check.

Please feel free to ask if there is any question. Thanks.

Huiyin

schoofe notifications@github.com 於 2019年6月28日 上午1:10 寫道：

Many thanks to the Nesvizhskii lab for releasing these awesome tools!

I'd be very keen on running MSFragger through our PD2.2 server, and managed to get the nodes up and running. The only problem is when trying a search (using a .mzml input file converted from a Thermo .raw file), the processing workflow errors out as it cannot find the .pepxml file that should be located in the "temp" folder. The only files present in this folder at that point are "fragger.params", the actual FASTA file and the .pepindex for that FASTA file.

Any input as to what I can do to debug this issue would be really appreciated, many thanks.

PD2.2 running on Windows 7, 64bit

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[schoofe]

Dear Huiyin,

Many thanks for your quick response; FragPipe reports the following on Java:

Java Info: 1.8.0_201, Java HotSpot (TM) 64-Bit Server VM, Oracle Corporation

I can also see a popup of MSFragger running when starting the search, but as soon as that popup window closes, the search stops with error message pointing out that the .pepXML is missing.

Any additional suggestions would be much appreciated, thanks.

[huiyinc]

Hi~

Thanks very mcuh for your feedback. We have released a new version of MSFragger-PD node last Friday. It will be great if you could download the new version and try it. It is recommanded to close and restart PD before running the new version of MSFragger-PD node.

If you still have the same error message: can't find the pepXML files, could you please send me the PD MagellanServer.log file? You may find the log file in: C:\ProgramData\Thermo\Proteome Discoverer 2.2\Logs by default. Please feel free to ask if you have any question.

Thank you.

Have a good day.

Huiyin

schoofe notifications@github.com 於 2019年7月1日 週一 上午12:08寫道：

Dear Huiyin,

Many thanks for your quick response; FragPipe reports the following on Java:

Java Info: 1.8.0_201, Java HotSpot (TM) 64-Bit Server VM, Oracle Corporation

I can also see a popup of MSFragger running when starting the search, but as soon as that popup window closes, the search stops with error message pointing out that the .pepXML is missing.

Any additional suggestions would be much appreciated, thanks.

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[schoofe]

Dear Huiyin,

Thanks for the heads up; I downloaded the update (very nice you now also support .raw files! :)), but unfortunately I still end up with the same error, albeit it it seems to appear a little later. I can see from the popup that MSFragger is running for a while, but then the Spectrum Selector process in the Processing workflow stops working at 88%. I've attached the PD MagellanServer.log file for your perusal.

Many thanks and all the best, Erwin MagellanServer.log

[huiyinc]

Hi Erwin,

Thanks very much for your reply. I have checked your log file and noticed that you use MSFragger-20190523.jar. However, only the latest version of MSFragger (MSFragger-20190628.zip) supports database search using RAW files. Could you please download the latest version of MSFrager and try it again? Here is the MSFragger download link: https://msfragger.arsci.com/upgrader/

If you still have the same issue, could you please share me your RAW file and fasta file so I can take a look of it? Thanks for your help.

Have a nice day.

Huiyin

schoofe notifications@github.com 於 2019年7月3日 週三 上午3:52寫道：

Dear Huiyin,

Thanks for the heads up; I downloaded the update (very nice you now also support .raw files! :)), but unfortunately I still end up with the same error, albeit it it seems to appear a little later. I can see from the popup that MSFragger is running for a while, but then the Spectrum Selector process in the Processing workflow stops working at 88%. I've attached the PD MagellanServer.log file for your perusal.

Many thanks and all the best, Erwin MagellanServer.log https://github.com/Nesvilab/MSFragger/files/3353804/MagellanServer.log

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[schoofe]

Hi Huiyin,

I can confirm that with the new PDnode file and the updated MSFragger-20190628, everything is working well! :)

Amazing performance as you've cut the search time in half, while generating more identifications. I'm very impressed.

Thanks for the great support and have a nice day. best, Erwin

[anesvi]

Great to see that resolved and working well. Alexey

Sent from my iPhone

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Hi Huiyin,

I can confirm that with the new PDnode file and the updated MSFragger-20190628, everything is working well! :)

Amazing performance as you've cut the search time in half, while generating more identifications. I'm very impressed.

Thanks for the great support and have a nice day. best, Erwin

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[huiyinc]

Hi Erwin,

It’s so good to hear that MSFragger-PD node works well on your computer. Please feel free to ask if you have any question.

Happy holiday!

Huiyin

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Alexey Nesvizhskii notifications@github.com 於 2019年7月4日 上午10:31 寫道：

Great to see that resolved and working well. Alexey

Sent from my iPhone

On Jul 3, 2019, at 9:19 PM, schoofe notifications@github.com<mailto:notifications@github.com> wrote:

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Hi Huiyin,

I can confirm that with the new PDnode file and the updated MSFragger-20190628, everything is working well! :)

Amazing performance as you've cut the search time in half, while generating more identifications. I'm very impressed.

Thanks for the great support and have a nice day. best, Erwin

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[paul-abraham]

All, Unfortunately, I am having the same issue despite using MSFragger-20190628 for PDv23 and I haven't been able to resolve the issue. Log_magellan_server.txt

Regards, Paul

[huiyinc]

Hi Paul,

Thanks for sharing us this message. Yes, it is the same issue that no interact.pep.xml file is generated. Could you please tell me which version of Philosopher you use? Thank you.

Huiyin

paul-abraham notifications@github.com 於 2019年7月5日 週五 下午1:45寫道：

All, Unfortunately, I am having the same issue despite using MSFragger-20190628 for PDv23 and I haven't been able to resolve the issue. Log_magellan_server.txt https://github.com/Nesvilab/MSFragger/files/3363648/Log_magellan_server.txt

Regards, Paul

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[paul-abraham]

Hi Huiyin,

I'm using philosopher_v1.2.3_windows_amd64.

Regards, Paul

[huiyinc]

Hi Paul,

Thanks for your quick reply.

I have tried the open search with an mzML file from HEK293 data set (I use MSFragger-20190628 and philosopher_v1.2.3_windows_amd6; 18G RAM), and there is no problem in the process. Since open search requires much larger memory than closed search, one possible reason is because of the insufficient memory. Could you please tell me the memory size of your computer and share me your RAW file, if possible?

Also, could you please run the open search using one of file from HEK293 data set (link http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001468) to check if you can run open search in your PD? Thank you very much for the help.

Huiyin

paul-abraham notifications@github.com 於 2019年7月5日 週五 下午1:57寫道：

Hi Huiyin,

I'm using philosopher_v1.2.3_windows_amd64.

Regards, Paul

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[paul-abraham]

Hi Huiyin,

I have 64GB of ram available and set it to 32GB. I downloaded b1906_293T_proteinID_01A_QE3_122212.raw and processed it with the human reference database from UniProt. The processing step resulted in the same error. If you can email me outside of GitHub, I will provide a link to the .raw file and .fasta

Regards, Paul

From: chuiyin notifications@github.com Sent: Friday, July 5, 2019 3:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Abraham, Paul abrahampe@ornl.gov; Comment comment@noreply.github.com Subject: [EXTERNAL] Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

Hi Paul,

Thanks for your quick reply.

I have tried the open search with an mzML file from HEK293 data set (I use MSFragger-20190628 and philosopher_v1.2.3_windows_amd6; 18G RAM), and there is no problem in the process. Since open search requires much larger memory than closed search, one possible reason is because of the insufficient memory. Could you please tell me the memory size of your computer and share me your RAW file, if possible?

Also, could you please run the open search using one of file from HEK293 data set (link http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001468) to check if you can run open search in your PD? Thank you very much for the help.

Huiyin

paul-abraham notifications@github.com<mailto:notifications@github.com> 於 2019年7月5日 週五 下午1:57寫道：

Hi Huiyin,

I'm using philosopher_v1.2.3_windows_amd64.

Regards, Paul

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

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[huiyinc]

Hi Paul,

Thanks for telling me the information. Here is my email address: dr.chuiyin@gmail.com Please feel free to email me your files. Thank you.

Huiyin

paul-abraham notifications@github.com 於 2019年7月8日 週一 上午10:23寫道：

Hi Huiyin,

I have 64GB of ram available and set it to 32GB. I downloaded b1906_293T_proteinID_01A_QE3_122212.raw and processed it with the human reference database from UniProt. The processing step resulted in the same error. If you can email me outside of GitHub, I will provide a link to the .raw file and .fasta

Regards, Paul

From: chuiyin notifications@github.com Sent: Friday, July 5, 2019 3:21 PM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Abraham, Paul abrahampe@ornl.gov; Comment < comment@noreply.github.com> Subject: [EXTERNAL] Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

Hi Paul,

Thanks for your quick reply.

I have tried the open search with an mzML file from HEK293 data set (I use MSFragger-20190628 and philosopher_v1.2.3_windows_amd6; 18G RAM), and there is no problem in the process. Since open search requires much larger memory than closed search, one possible reason is because of the insufficient memory. Could you please tell me the memory size of your computer and share me your RAW file, if possible?

Also, could you please run the open search using one of file from HEK293 data set (link http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001468) to check if you can run open search in your PD? Thank you very much for the help.

Huiyin

paul-abraham notifications@github.com<mailto:notifications@github.com> 於 2019年7月5日 週五 下午1:57寫道：

Hi Huiyin,

I'm using philosopher_v1.2.3_windows_amd64.

Regards, Paul

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.

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[schoofe]

Hi Huiyin,

Could it be that there is an issue running multiple files, located in the same folder, in batch mode (in PD2.2)? I wanted to run 6 files in one batch, creating a results file for each individual .raw file, but ended up getting the same .pepXML error message, causing all the runs to fail. My first thought was that perhaps the 'temp' folder gets overwritten/deleted by one run, causing the others to fail? Running the 6 files independently seems to work fine. Many thanks, Erwin

[huiyinc]

Hi Erwin,

Thanks very much for your effort on testing our MSFragger-PD node. Could you please tell me how you run the 6 files? Do you create 6 processing workflows (as shown in Figure 1; each with a input file) or run the 6 files in one processing workflows (as shown in Figure 2)? [image: image.png] Figure 1. Two processing workflows, each with a input file

[image: image.png] Figure 2. One processing workflows with two input files.

If it is the first case, I am sorry that our MSFragger-PD node currently does not support multiple processing workflow because it requires different processing structures for it. However, you could run the 6 files in one processing workflow, and it should work well. We will add the multiple processing workflows in our future updates. Please let me know if this answers your question. Thank you.

Huiyin

schoofe notifications@github.com 於 2019年7月9日 週二 上午2:54寫道：

Hi Huiyin,

Could it be that there is an issue running multiple files, located in the same folder, in batch mode (in PD2.2)? I wanted to run 6 files in one batch, creating a results file for each individual .raw file, but ended up getting the same .pepXML error message, causing all the runs to fail. My first thought was that perhaps the 'temp' folder gets overwritten/deleted by one run, causing the others to fail? Running the 6 files independently seems to work fine. Many thanks, Erwin

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[MetalPoldi]

Hi all,

I'm having the same issues as @paul-abraham : PD 2.3 on Win10, 16 GB RAM MSFragger 20190628 Philosopher 1.4.6 windows amd64 and .pepXML is missing. Log_magellan_server.txt

Any ideas or could you provide the solution how Pauls problem was solved?

Thanks,

Dierk

[fcyu]

Hi Dierk,

Just to make sure: you set a NONSPECIFIC open search, right? If so, how much memory does your computer have?

Best,

Fengchao

[huiyinc]

Hi Dierk,

The reason why Fengchao ask this question is because MSFragger needs at least 64GB available/free memory for closed search with nonspecific digestion (peptide Length: 7 to 30). So you need more memory if you want to perform open search with nonspecific digestion. Please feel free to ask if you have any question. Thanks.

Huiyin

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Fengchao notifications@github.com 於 2019年7月29日 上午9:10 寫道：

Hi Dierk,

Just to make sure: you set a NONSPECIFIC open search, right? If so, how much memory does your computer have?

Best,

Fengchao

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[anesvi]

Yuo would need to use FragPipe with Split option if you would like to do nonspecific digestion allowing longer peptides and/or many PTMs.

Also, open + nonspecific is a very challenging analysis, and may not be the best option depending on what you are trying to achieve. Perhaps you can contact us and explain what you would like to do.

Best, Alexey

From: chuiyin [mailto:notifications@github.com] Sent: Monday, July 29, 2019 9:25 AM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

External Email - Use Caution Hi Dierk,

The reason why Fengchao ask this question is because MSFragger needs at least 64GB available/free memory for closed search with nonspecific digestion (peptide Length: 7 to 30). So you need more memory if you want to perform open search with nonspecific digestion. Please feel free to ask if you have any question. Thanks.

Huiyin

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Fengchao notifications@github.com<mailto:notifications@github.com> 於 2019年7月29日 上午9:10 寫道：

Hi Dierk,

Just to make sure: you set a NONSPECIFIC open search, right? If so, how much memory does your computer have?

Best,

Fengchao

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[MetalPoldi]

Sorry,

I accidentally uploaded the log from Paul. Here's mine: MagellanServer.log I used the predefined workflows (consensus & processing) for closed searches with Philosopher and default parameters.

Thanks,

Dierk

[fcyu]

Hi Dierk,

I saw that MSFragger ran for only 1 sec (2019-07-29 15:30:49,779 INFO [Thread for job (ID: 20)] MSFraggerPDv23.MSFragger - (20-7) MSFragger Running Time --0:0:1, @huiyinc Am I right?). Looks like it stopped before doing any search.

Here is my random guess: Did you put the ext folder to the folder where MSFragger is?

Best,

Fengchao

[MetalPoldi]

Hey Fengchao, unfortunately not. The MSFragger.jar is in the same folder as the ext-folder.

Thanks,

Dierk

[anesvi]

Have you tried to run using FragPipe (and not in PD) using the same parameters?

Fengchao, Hui-yin – is there way to see the log from MSFragger when running in PD? When it crashed so fast there is usually wrong database (not found) or a problem with the input data

From: MetalPoldi [mailto:notifications@github.com] Sent: Monday, July 29, 2019 10:54 AM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

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Hey Fengchao, unfortunately not. The MSFragger.jar is in the same folder as the ext-folder.

Thanks,

Dierk

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[huiyinc]

@Nesvizhskii, Alexey nesvi@med.umich.edu Yes, that's what I am working on now: printing the error message in PD. It will be included in our next release. Thanks. Huiyin

Alexey Nesvizhskii notifications@github.com 於 2019年7月29日 週一 上午11:27寫道：

Have you tried to run using FragPipe (and not in PD) using the same parameters?

Fengchao, Hui-yin – is there way to see the log from MSFragger when running in PD? When it crashed so fast there is usually wrong database (not found) or a problem with the input data

From: MetalPoldi [mailto:notifications@github.com] Sent: Monday, July 29, 2019 10:54 AM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment < comment@noreply.github.com> Subject: Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

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Hey Fengchao, unfortunately not. The MSFragger.jar is in the same folder as the ext-folder.

Thanks,

Dierk

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[huiyinc]

Hi Dierk,

Could you please run the MSFragger via command lines and send us the message you get? Here are the instructions:

1. Enter cmd.exe in the Search box on the Taskbar.
2. Copy and paste this command: java -jar -Xmx16G C:\MSFragger-20190628\MSFragger-20190628.jar C:\Users\COMPUTER\Desktop\20181127_006\temp\fragger.params C:\Users\COMPUTER\Desktop\20181127_006.raw
3. Press "enter".

Thanks.

Huiyin

MetalPoldi notifications@github.com 於 2019年7月29日 週一 上午10:54寫道：

Hey Fengchao, unfortunately not. The MSFragger.jar is in the same folder as the ext-folder.

Thanks,

Dierk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWAZPVHEBSOQ5GCITIZ3QB4ACJA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3A67DA#issuecomment-516026252, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA7ENF5BQGWWACAVCC3QB4ACJANCNFSM4H4CFHOA .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[MetalPoldi]

I just realized that I installed a wrong version of java. Now it's working in command line and as a PD node. Thanks for all the quick help!

[fcyu]

You are welcome.

Best,

Fengchao

[schoofe]

Hi Erwin, Thanks very much for your effort on testing our MSFragger-PD node. Could you please tell me how you run the 6 files? Do you create 6 processing workflows (as shown in Figure 1; each with a input file) or run the 6 files in one processing workflows (as shown in Figure 2)? [image: image.png] Figure 1. Two processing workflows, each with a input file [image: image.png] Figure 2. One processing workflows with two input files. If it is the first case, I am sorry that our MSFragger-PD node currently does not support multiple processing workflow because it requires different processing structures for it. However, you could run the 6 files in one processing workflow, and it should work well. We will add the multiple processing workflows in our future updates. Please let me know if this answers your question. Thank you. Huiyin schoofe notifications@github.com 於 2019年7月9日 週二 上午2:54寫道： … Hi Huiyin, Could it be that there is an issue running multiple files, located in the same folder, in batch mode (in PD2.2)? I wanted to run 6 files in one batch, creating a results file for each individual .raw file, but ended up getting the same .pepXML error message, causing all the runs to fail. My first thought was that perhaps the 'temp' folder gets overwritten/deleted by one run, causing the others to fail? Running the 6 files independently seems to work fine. Many thanks, Erwin — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#31?email_source=notifications&email_token=ALAWWA7DIWPBKM7TIATFMWLP6QY2NA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZPJGPA#issuecomment-509514556>, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA7J2KXIFNP2HVBPTQLP6QY2NANCNFSM4H4CFHOA . -- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

Dear Huiyin,

Finally got a chance to get back to this, as I'm still experiencing the issue when trying to analyze multiple files as a batch analysis. If I understood your question correctly, I have 1 processing and 1 consensus flow, and I just add multiple .raw files to the "files for analysis" box. When I search those 2 files without checking "As batch", it works fine as it creates one result file. However, when I activate the "As batch" checkbox, thus searching the 2 files independently (located in the same windows folder), the search crashes as before.

Hopefully this helps to get to the bottom of this as I often like to search files as batches to get a unique results file for each .raw file.

many thanks, Erwin

[huiyinc]

Hi Erwin,

Thanks very much for checking it. Yes, as discussed in the previous email, our MSFragger-PD node currently doesn't support batch processing workflows. Please run the processing workflow sequentially. We are going to release a new version of MSFragger-PD node which supports the batch processing workflow soon. It will be great if you could try it and give us your valuable feedback. Thank you.

Have a good day.

Huiyin

schoofe notifications@github.com 於 2019年8月28日 週三 上午7:49寫道：

Hi Erwin, Thanks very much for your effort on testing our MSFragger-PD node. Could you please tell me how you run the 6 files? Do you create 6 processing workflows (as shown in Figure 1; each with a input file) or run the 6 files in one processing workflows (as shown in Figure 2)? [image: image.png] Figure 1. Two processing workflows, each with a input file [image: image.png] Figure 2. One processing workflows with two input files. If it is the first case, I am sorry that our MSFragger-PD node currently does not support multiple processing workflow because it requires different processing structures for it. However, you could run the 6 files in one processing workflow, and it should work well. We will add the multiple processing workflows in our future updates. Please let me know if this answers your question. Thank you. Huiyin schoofe notifications@github.com 於 2019年7月9日 週二 上午2:54寫道： … <#m2490794621997819681> Hi Huiyin, Could it be that there is an issue running multiple files, located in the same folder, in batch mode (in PD2.2)? I wanted to run 6 files in one batch, creating a results file for each individual .raw file, but ended up getting the same .pepXML error message, causing all the runs to fail. My first thought was that perhaps the 'temp' folder gets overwritten/deleted by one run, causing the others to fail? Running the 6 files independently seems to work fine. Many thanks, Erwin — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#31 https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWA7DIWPBKM7TIATFMWLP6QY2NA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZPJGPA#issuecomment-509514556>, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA7J2KXIFNP2HVBPTQLP6QY2NANCNFSM4H4CFHOA . -- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

Dear Huiyin,

Finally got a chance to get back to this, as I'm still experiencing the issue when trying to analyze multiple files as a batch analysis. If I understood your question correctly, I have 1 processing and 1 consensus flow, and I just add multiple .raw files to the "files for analysis" box. When I search those 2 files without checking "As batch", it works fine as it creates one result file. However, when I activate the "As batch" checkbox, thus searching the 2 files independently (located in the same windows folder), the search crashes as before.

Hopefully this helps to get to the bottom of this as I often like to search files as batches to get a unique results file for each .raw file.

many thanks, Erwin

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWA2HACY7H5DPSSTL6Y3QGZQ4DA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5K27CI#issuecomment-525709193, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWAZLRSCPWZZMFXGKSILQGZQ4DANCNFSM4H4CFHOA .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[schoofe]

Hi Huiyin,

Ok thanks, and sorry for misunderstanding your original email. I will patiently await the next release while submitting jobs sequentially for now.

all the best, Erwin

[huiyinc]

Hi Erwin,

We just release the new version of our MSFragger-PD node, which supports the batch processing workflows. It will be great if you could try it and give us your valuable feedback! Please don't hesitate to email us if you have any question.

Have a good day.

Huiyin

schoofe notifications@github.com 於 2019年8月29日 週四 上午4:29寫道：

Hi Huiyin,

Ok thanks, and sorry for misunderstanding your original email. I will patiently await the next release while submitting jobs sequentially for now.

all the best, Erwin

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWA3YK3737ADKXIFGWXTQG6CH7A5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5NWKFA#issuecomment-526083348, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA75N5C5R2YMLR4ROJDQG6CH7ANCNFSM4H4CFHOA .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[schoofe]

Hi Huiyin,

Thanks for the notification, and now after having tried a variety of scenarios, can confirm everything seems to be running beautifully now. Well done on an amazing piece of software and I look forward to exploring its utility in many of our on-going projects! :) best, Erwin

[huiyinc]

Hi Erwin,

It's great to hear that. Please feel free to ask if you have any question using our MSFragger-PD node. Thanks.

Have a good day.

Huiyin

schoofe notifications@github.com 於 2019年9月18日 週三 上午2:05寫道：

Hi Huiyin,

Thanks for the notification, and now after having tried a variety of scenarios, can confirm everything seems to be running beautifully now. Well done on an amazing piece of software and I look forward to exploring its utility in many of our on-going projects! :) best, Erwin

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWA6FSFQFDPQD3JES3O3QKHAJFA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD665BBY#issuecomment-532533383, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA2F3YIRZNWBTTAGDUDQKHAJFANCNFSM4H4CFHOA .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[anesvi]

Dear Erwin,

Thank you for using the tools. If you have any feedback on the tools, that would be very much appreciated. I think one area we are still trying to understand is how well open search works within PD. There could be some issues.

Best, Alexey

From: chuiyin [mailto:notifications@github.com] Sent: Wednesday, September 18, 2019 10:52 AM To: Nesvilab/MSFragger MSFragger@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/MSFragger] .pepXML not found using PDnode (PD2.2) (#31)

External Email - Use Caution Hi Erwin,

It's great to hear that. Please feel free to ask if you have any question using our MSFragger-PD node. Thanks.

Have a good day.

Huiyin

schoofe notifications@github.com<mailto:notifications@github.com> 於 2019年9月18日 週三 上午2:05寫道：

Hi Huiyin,

Thanks for the notification, and now after having tried a variety of scenarios, can confirm everything seems to be running beautifully now. Well done on an amazing piece of software and I look forward to exploring its utility in many of our on-going projects! :) best, Erwin

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/31?email_source=notifications&email_token=ALAWWA6FSFQFDPQD3JES3O3QKHAJFA5CNFSM4H4CFHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD665BBY#issuecomment-532533383, or mute the thread https://github.com/notifications/unsubscribe-auth/ALAWWA2F3YIRZNWBTTAGDUDQKHAJFANCNFSM4H4CFHOA .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

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